LuckyBoyAK @Justin Thanks. I can see the issue now.
The issue is with models that are attachments only that are also attached to a model that has attachments.

In this screenshot, this is me about to upload a test model but I can already see an issue.
"obj1" is not listed and I assume will not be uploaded.
"objmain" is a empty model with only attachpoints attaching "obj2" and "obj1holder".
"obj2" is a model attached to "objmain"
"obj1holder" is an empty model with only attach points, attaching "obj1"
The upload is not finding/uploading the model two nests away. (obj1)
Here's a diagram to best explain the attachment heirarchy.

Main is just attach points, 2 is a model, holder is just attach points, 1 is a model.
1 is not being uploaded.